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Fix data-loss and alignment defects from the post-1.2.0 audit (plan A) - #74

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fix-audit-data-safety

Commits on Oct 1, 2026
- Record the post-1.2.0 audit and plan its remediation
  
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  9aed4a9
- Reorient reverse-strand genomes in the MAFFT backend
  
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  38428df
- Compare the reassort alignment-fraction filter in percent
  
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  9e87d01
- Keep reassort segment scans inside their own directories
  
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  4183ec3
- Curate only downloaded genomes in find-references
  
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  4a69edf
- Curate before each build and align the last round's downloads in fill-references
  
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  97fe19c
- Keep uncovered contigs and unplaced genomes in MAF-derived alignments
  
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  bcee496
- Name progressiveMauve rows from the staged genome label
  
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  370e266
- Clean whitespace from staged genomes and report malformed input by file
  
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  57d0bf0
- Document the data-safety and alignment fixes
  
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  6f3bdc2
- Address the plan A review: protect the reference, name every all-gap row, guard the working copy
  
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- Record the plan A review outcome in the audit spec
  
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  35d9e19